we're at the age just before assembly programming. we'll start amassing a library of standard plays -- instructions in asm -- then start building higher level "languages". Then design of beings will be a programming activity.

Ethanol is a perfectly viable bio fuel as is vegetable oil... modern diesel engines are practically designed not to run on vegetable oil on purpose to prevent people from burning alternative fuels. While every major auto manufacturer makes ethanol burning vehicles and sells them in Brazil while the ones sold here are designed not to be able to burn fuel that is primarily ethanol.

Modifications to modern diesels to run veg oil would be trivial.... and its a better lubricant than diesel.

What is not viable is *corn* ethanol... because corn doesn't even make enough energy to be net positive, I mean even when people digest it it mostly goes unused.

And of course the morons at large downvote sheesh. Electric cars are not THE ANSWER, the are merely part of it, and even they rely on other things falling into place for them to be clean.

we're at the age just before assembly programming. we'll start amassing a library of standard plays -- instructions in asm -- then start building higher level "languages". Then design of beings will be a programming activity.

If that was even remotely close to how organisms work, we'd be there already.

Computers were deliberately designed to BE programmable. Organisms evolved to function and reproduce in a particular environment, without the advantage of particular things critical to human engineering progress: field replacement of malfunctioning parts and incremental upgrades. Organisms do not have an application programming interface.

The article above is a good account of what has to actually be done to modify an organism to do something so wildly at variance with what it evolved to do. Note how it in no way resembles coding. It's not even the result of a design process as such; it's a bunch of tuning tweaks plus an environmental hack to keep the resulting critter from poisoning itself to death.

If we have to re-engineer both our engines and our infrastructure in order to use it to replace fossil fuels

???

Ethanol is already blended with gasoline at most pumps across the nation. Most everyone already fills up on E10, there's no infrastructure change necessary unless you plan on storing pure ethanol in these same tanks. Which nobody does, because ethanol doesn't combust well at low temperatures, so the best you'll find most anywhere is E85, and E70 in the winter.

There's nothing else for us to re-engineer, our cars can already run ethanol without modification. The only thing most cars need is injector mappings for high ethanol blends like E85 and E99, which is where the Flex Fuel badges came from. There's no physical or functional difference between conventional gasoline and ethanol motors.

After getting basic ability working, they should select like crazy for fuel production and try to let evolution do the rest. See what happens!

As noted in the article, the fuel molecules are toxic to the cell, it's going to be hard/impossible to find a way to select for better fuel production. These molecules just aren't needed for the yeast to survive so there's likely no sane way to apply evolutionary pressure.

Are we we not going to get an Ars article about robots being built from stem cells that grow their own hearts and walk around? It’s quite horrifically creepy and I’m not sure what to make of it all. But it seems the perfect Ars topic.

we're at the age just before assembly programming. we'll start amassing a library of standard plays -- instructions in asm -- then start building higher level "languages". Then design of beings will be a programming activity.

If that was even remotely close to how organisms work, we'd be there already.

Computers were deliberately designed to BE programmable. Organisms evolved to function and reproduce in a particular environment, without the advantage of particular things critical to human engineering progress: field replacement of malfunctioning parts and incremental upgrades. Organisms do not have an application programming interface.

The article above is a good account of what has to actually be done to modify an organism to do something so wildly at variance with what it evolved to do. Note how it in no way resembles coding. It's not even the result of a design process as such; it's a bunch of tuning tweaks plus an environmental hack to keep the resulting critter from poisoning itself to death.

You're not wrong, but you're also describing something not that different from legacy software maintenance/improvement. Extending a system against its original purpose? Check. Adding a whatever hacks will make it work both in and around the system? Check. Setting up a special environment to meet its unusual needs? Check!

I think OP's timeline is not correct at all but I do also think there's a pretty good parallel to be made. We're still working at a very low level. Eventually we will be able to work with the equivalent of genetic frameworks and libraries. Note that in this case they even imported some DNA from another project!

So, granted this is hard. But isn't it only hard once? After you've figured out how to produce yeasty gasoline, or whatever, your new yeast will reproduce itself as long as you keep feeding it. Your amortized development costs go to zero.

Cost problems would arise if care, feeding, and final refinement are expensive.

So, granted this is hard. But isn't it only hard once? After you've figured out how to produce yeasty gasoline, or whatever, your new yeast will reproduce itself as long as you keep feeding it. Your amortized development costs go to zero.

Cost problems would arise if care, feeding, and final refinement are expensive.

The hard part is finding yeast/algae/bacteria that apart from producing hydrocarbons are also fast growing enough to outcompete their cousins that would naturally filter into the production tanks.

After getting basic ability working, they should select like crazy for fuel production and try to let evolution do the rest. See what happens!

As noted in the article, the fuel molecules are toxic to the cell, it's going to be hard/impossible to find a way to select for better fuel production. These molecules just aren't needed for the yeast to survive so there's likely no sane way to apply evolutionary pressure.

we're at the age just before assembly programming. we'll start amassing a library of standard plays -- instructions in asm -- then start building higher level "languages". Then design of beings will be a programming activity.

If that was even remotely close to how organisms work, we'd be there already.

Computers were deliberately designed to BE programmable. Organisms evolved to function and reproduce in a particular environment, without the advantage of particular things critical to human engineering progress: field replacement of malfunctioning parts and incremental upgrades. Organisms do not have an application programming interface.

The article above is a good account of what has to actually be done to modify an organism to do something so wildly at variance with what it evolved to do. Note how it in no way resembles coding. It's not even the result of a design process as such; it's a bunch of tuning tweaks plus an environmental hack to keep the resulting critter from poisoning itself to death.

You're not wrong, but you're also describing something not that different from legacy software maintenance/improvement. Extending a system against its original purpose? Check. Adding a whatever hacks will make it work both in and around the system? Check. Setting up a special environment to meet its unusual needs? Check!

I think OP's timeline is not correct at all but I do also think there's a pretty good parallel to be made. We're still working at a very low level. Eventually we will be able to work with the equivalent of genetic frameworks and libraries. Note that in this case they even imported some DNA from another project!

edit: fix a typo

He’s really just wrong. It’s like saying quantum computing is not computing because there are no binary bits and the code looks really different. So what? Omg, the way we eventually code with biology is really different! Oh noes. It’s still going to be algorithms you string together. Libraries someone else built that you use as is or modify.

It is missing the part where it’s all about the abstract algorithms, the actual instantiation is a separate matter. That universe of potential algorithms is vast and it most certainly includes stuff you can run in a cell or organism.

There are actually articles about scientists going about trying to figure out the equivalent of algorithms and code. The only substantially different thing is that you are coding for manufacturing systems that later have other behaviors that emerge from how they work together. Is it in any way different from Conway’s game of life? No, just more complex.

So, granted this is hard. But isn't it only hard once? After you've figured out how to produce yeasty gasoline, or whatever, your new yeast will reproduce itself as long as you keep feeding it. Your amortized development costs go to zero.

Cost problems would arise if care, feeding, and final refinement are expensive.

I suspect that the ongoing maintenance will be a hassle. Your organism doesn't stop evolving just because it's engineered; and what you are engineering for is a brutally maladaptive trait("spend massive amounts of energy synthesizing molecules you don't use until they poison you" is not the strategy of champions).

In a suitably supportive environment such an organism can survive; but it will be swiftly out-competed by any mutants that manage to stub out your alterations, start metabolizing the fuel you wanted left intact as a final product, etc.

Doesn't mean you'll need to re-engineer it every time, probably just keep known-good samples on ice and periodically purge the grow tanks and recolonize them from backups; but expecting stability from microorganisms is unrealistic; markedly more so when you want them to do something more or less actively self-destructive.

Easy to control. They'll be oozing gasoline, so just toss a match at the infected and kill 'em with fire.

So, when the zombie apocalypse comes we should engineer this bacteria to bond to whatever causes the zombies?

That should help.

What the heck? No. You use it to make precious fuel for your zombie mobile! Don’t be the sucker that failed to secure an BEV vehicle + solar charging scheme or ICE vehicle with plentiful sweet smelling dinosaur distillate. This is your moment as a preppier to shine! Why would you want to ruin it?

Cool. But we should really focus on weaning ourselves off carbon based fuels.

While true, there will always be some type of transportation where a stored energy source is required. For example, an airplane would need a pretty long extension cord. Ships also require stored energy, long haul trucking, and sparsely populated areas, such as Arctic and Antarctic as well as parts of North America.

Until energy storage can approximate a tank of gas, it will be at a disadvantage to easy acceptance.

Ethanol is a perfectly viable bio fuel as is vegetable oil... modern diesel engines are practically designed not to run on vegetable oil on purpose to prevent people from burning alternative fuels. While every major auto manufacturer makes ethanol burning vehicles and sells them in Brazil while the ones sold here are designed not to be able to burn fuel that is primarily ethanol.

Modifications to modern diesels to run veg oil would be trivial.... and its a better lubricant than diesel.

What is not viable is *corn* ethanol... because corn doesn't even make enough energy to be net positive, I mean even when people digest it it mostly goes unused.

Hardly. Commercial Diesel engines don't run on vegetable oil because of emissions standards. Diesel engine and exhaust designers go to great lengths to design their engines to minimize toxic byproducts and particulate pollution based on a known quality of fuel. You don't get a known quality of input from vegetable oil. And good luck rolling out the infrastructure to get that kind of known quality of input. You'd have to repurpose land, convince farmers (family and corportate) it's worth their time and investment in resources, scale up any production capacity to meet whatever demand there might be, deal with any potentially unforeseen consequences in the manufacturing process, transport the product, and then make it available to truckers and transportation in the same way Diesel is now. At this point you might as well just transition entirely to electric transportation because by the time you did all that, electric cargo transport would already have passed you up.

Second, the reason ethanol vehicles are sold in Brazil is because the country mandates their use to keep their reliance on foreign oil supplies as low as they can. It has nothing to do with efficiency: E85 doesn't get you better mileage, it gets you more power. The mileage is actually worse versus pure gasoline. That doesn't actually make sense in the US, from an economic policy point, because we're currently a net exporter of petroleum thanks to all those federal petroleum reservations mandated in the Carter era now being opened up for exploration and use. In many areas of the US, you might own an E85 capable vehicle, but you sure can't find gas for it! It's not economically viable in those areas even if there was a workable market.

Will that change again in 10 or 15 years? Perhaps, and if it does the economics of ethanol will be revisited. But for now, you're hollering and no one is going to listen. And there's no way that political and economic equation is going to change in the US any time soon. People have to get to work, they have to get kids to activities, and not everyone lives in dense urban areas where public transportation or walking is viable, nor should they have to.

So, granted this is hard. But isn't it only hard once? After you've figured out how to produce yeasty gasoline, or whatever, your new yeast will reproduce itself as long as you keep feeding it. Your amortized development costs go to zero.

Cost problems would arise if care, feeding, and final refinement are expensive.

I suspect that the ongoing maintenance will be a hassle. Your organism doesn't stop evolving just because it's engineered; and what you are engineering for is a brutally maladaptive trait("spend massive amounts of energy synthesizing molecules you don't use until they poison you" is not the strategy of champions).

In a suitably supportive environment such an organism can survive; but it will be swiftly out-competed by any mutants that manage to stub out your alterations, start metabolizing the fuel you wanted left intact as a final product, etc.

Perhaps, but your contention is not entirely obvious. Brewer's yeast already waste a lot of energy making a fuel-like molecule and excreting it: ethanol. The likely evolutionary advantage is that yeast are more tolerant of ethanol than essentially any other organism.

Since the short-chain hydrocarbons these yeast are making seem to be toxic, they may help the modified yeast out-compete interloping organisms.

As with most issues in evolution, the "goal" is not to be the most efficient organism in existence. The "goal" is to continue to have offspring at rates comparable to or higher than any competitors. The researchers may need to add some explicit benefit to the products, but it sounds as though the current version may be able to grow unmolested with monitoring.

Because these are yeast and not algae or plants, the cultures will still need to be fed energetic molecules; I suspect that this is the real problem with the project. If algae were engineered to excrete toxic short-chain hydrocarbons using sunlight, water, and carbon dioxide as sources, they might be more useful than yeast, but this is an interesting start.

Are we we not going to get an Ars article about robots being built from stem cells that grow their own hearts and walk around? It’s quite horrifically creepy and I’m not sure what to make of it all. But it seems the perfect Ars topic.

Been wondering the same thing. My only guess is that they're trying to do an in-depth article about it.

We've created our first replicants. I'd always had a difficult time wrapping my head around a "manufactured biological machine" that was somehow different than just an animal clone. This made it very clear to me how you'd go about that.

So, granted this is hard. But isn't it only hard once? After you've figured out how to produce yeasty gasoline, or whatever, your new yeast will reproduce itself as long as you keep feeding it. Your amortized development costs go to zero.

Cost problems would arise if care, feeding, and final refinement are expensive.

I suspect that the ongoing maintenance will be a hassle. Your organism doesn't stop evolving just because it's engineered; and what you are engineering for is a brutally maladaptive trait("spend massive amounts of energy synthesizing molecules you don't use until they poison you" is not the strategy of champions).

In a suitably supportive environment such an organism can survive; but it will be swiftly out-competed by any mutants that manage to stub out your alterations, start metabolizing the fuel you wanted left intact as a final product, etc.

Perhaps, but your contention is not entirely obvious. Brewer's yeast already waste a lot of energy making a fuel-like molecule and excreting it: ethanol. The likely evolutionary advantage is that yeast are more tolerant of ethanol than essentially any other organism.

Since the short-chain hydrocarbons these yeast are making seem to be toxic, they may help the modified yeast out-compete interloping organisms.

As with most issues in evolution, the "goal" is not to be the most efficient organism in existence. The "goal" is to continue to have offspring at rates comparable to or higher than any competitors. The researchers may need to add some explicit benefit to the products, but it sounds as though the current version may be able to grow unmolested with monitoring.

Because these are yeast and not algae or plants, the cultures will still need to be fed energetic molecules; I suspect that this is the real problem with the project. If algae were engineered to excrete toxic short-chain hydrocarbons using sunlight, water, and carbon dioxide as sources, they might be more useful than yeast, but this is an interesting start.

Brewers' yeast also has a habit of getting out-competed if you aren't careful. It's totally doable without lab-grade precautions; but failure to sanitize things while brewing generally results in a substantially different collection of microbes(and taste) than you were hoping for, and brewing is usually done in relatively short batch processes, rather than long-running continuous ones, so evolutionary drift among your yeast isn't too serious a risk.

I expect that the same will be true of a situation like this: so long as your starting situation is clean and you terminate the batch periodically you'll be fine; but expecting it to maintain the equilibrium you want if run as a continuous process over the long term isn't going to fly.

Brewer's yeast already waste a lot of energy making a fuel-like molecule and excreting it: ethanol. The likely evolutionary advantage is that yeast are more tolerant of ethanol than essentially any other organism.

That struck me as way too pat. But stopping short of complete oxidation even when oxygen and the pathways are available does indeed happen. It's considered weird enough it gets its own effect name: the Crabtree effect.

Although some but not all of the energy left on the table remains available to the yeast. Wikipedia also points to a paper that notes (new to me!) that the yeast can change its mind later and burn the ethanol: Resurrecting ancestral alcohol dehydrogenases from yeast: "Yeast later consumes the accumulated ethanol, exploiting Adh2, an Adh1 homolog differing by 24 (of 348) amino acids. As many microorganisms cannot grow in ethanol, accumulated ethanol may help yeast defend resources in the fruit. . . Generating ethanol from glucose in the presence of dioxygen, only to then reoxidize the ethanol, is energetically expensive. For each molecule of ethanol converted to acetyl-coenzyme A, a molecule of ATP is used."

I would think that a modern version of the reverse flow system would work best with specialized yeast making changes and sending the results to the next stage. Trying to create super yeast that can do everything all on its own would take at least twice as long to perfect.

Easy to control. They'll be oozing gasoline, so just toss a match at the infected and kill 'em with fire.

So, when the zombie apocalypse comes we should engineer this bacteria to bond to whatever causes the zombies?

That should help.

What the heck? No. You use it to make precious fuel for your zombie mobile! Don’t be the sucker that failed to secure an BEV vehicle + solar charging scheme or ICE vehicle with plentiful sweet smelling dinosaur distillate. This is your moment as a preppier to shine! Why would you want to ruin it?

Time for a Syfy movie with zombie slayers wearing alligators on their pockets

But ethanol isn't a drop-in replacement for many current uses, which raises questions about its overall utility. If we have to re-engineer both our engines and our infrastructure in order to use it to replace fossil fuels, then there's not much space for a smooth transition away from gasoline and other liquid fuels.

Brazil called, and said that you should hold its sugarcane-derived high proof ethanol.

Easy to control. They'll be oozing gasoline, so just toss a match at the infected and kill 'em with fire.

So, when the zombie apocalypse comes we should engineer this bacteria to bond to whatever causes the zombies?

That should help.

What the heck? No. You use it to make precious fuel for your zombie mobile! Don’t be the sucker that failed to secure an BEV vehicle + solar charging scheme or ICE vehicle with plentiful sweet smelling dinosaur distillate. This is your moment as a preppier to shine! Why would you want to ruin it?

Well, I suppose you could refine zombies into gasoline. It'd probably involve a woodchipper, though.

Brewers' yeast also has a habit of getting out-competed if you aren't careful. It's totally doable without lab-grade precautions; but failure to sanitize things while brewing generally results in a substantially different collection of microbes than you were hoping for, and brewing is usually done in relatively short batch processes, rather than long-running continuous ones, so evolutionary drift among your yeast isn't too serious a risk.

There are two parts to your statement. The first is that yeast may be out-competed. This is true, if the culture is being started with a relatively small amount of yeast, because yeast grow slowly compared to most bacteria, and the selective advantage that yeast have in releasing ethanol only works if enough yeast are releasing ethanol to raise the local concentration to a range sufficient to limit the growth rate of the bacterial competitors.

Once the yeast have released enough ethanol, dealing with evolutionary modifications only matters among the yeast if the modified yeast have a growth advantage. This may require some tailoring of the yeast to allow for a growth advantage of some kind based upon the level of the short-chain hydrocarbon, but, again, yeast have developed the property of ethanol release and ethanol tolerance, and have not lost it over millions of generations.

Quote:

I expect that the same will be true of a situation like this: so long as your starting situation is clean and you terminate the batch periodically you'll be fine; but expecting it to maintain the equilibrium you want if run as a continuous process over the long term isn't going to fly.

This is less clear. For most brewing processes, a continuous process is difficult to manage, because ethanol (unlike most hydrocarbons) is water miscible. However, some brewers allow the yeast from one culture to settle out (or be centrifuged out) and use that culture for the next batch.

For non-water soluble hydrocarbons, a continuous process may be more efficient. And if the hydrocarbons are toxic to other organisms, those other contaminating organisms would have much less relevance, because the culture system would already have a high concentration of the toxic material to prevent the competition from occurring.

Brewer's yeast already waste a lot of energy making a fuel-like molecule and excreting it: ethanol. The likely evolutionary advantage is that yeast are more tolerant of ethanol than essentially any other organism.

That struck me as way too pat. But stopping short of complete oxidation even when oxygen and the pathways are available does indeed happen. It's considered weird enough it gets its own effect name: the Crabtree effect.

Although some but not all of the energy left on the table remains available to the yeast. Wikipedia also points to a paper that notes (new to me!) that the yeast can change its mind later and burn the ethanol: Resurrecting ancestral alcohol dehydrogenases from yeast: "Yeast later consumes the accumulated ethanol, exploiting Adh2, an Adh1 homolog differing by 24 (of 348) amino acids. As many microorganisms cannot grow in ethanol, accumulated ethanol may help yeast defend resources in the fruit. . . Generating ethanol from glucose in the presence of dioxygen, only to then reoxidize the ethanol, is energetically expensive. For each molecule of ethanol converted to acetyl-coenzyme A, a molecule of ATP is used."

(Edited to correct "some but all" to "some but not all".)

The energy lost in making ethanol is significant; pyruvate decarboxylase converts pyruvate to acetaldehyde with loss of carbon dioxide but without generation of NADH. This is followed by the alcohol dehydrogenase conversion of acetaldehyde to ethanol with conversion of NADH (generated in glycolysis) back to NAD.

Since each NADH is worth 2 to 3 ATP, conversion to ethanol wastes that much ATP as a minimum.

Alcohol dehydrogenase is reversible, so, if the concentration of ethanol outside the cell is high enough, it is possible for the ethanol to be imported and converted to acetyl-CoA (with, as you noted, the cost of an ATP). However, the NADH that is lost by not using pyruvate dehydrogenase is not recoverable. And maintaining an ethanol content in the environment sufficient to dissuade competing organisms required a permanent loss of vast majority of the energy content present in the original carbohydrate, as well as the use of the carbons in the carbohydrate for synthesizing other useful molecules.

Producing ethanol is a waste of resources for yeast. There is an evolutionary benefit by eliminating the potential for competition, but the yeast have to expend resources to do so.

The work described in the article would allow another system in which the yeast would expend resources in order to be able to reproduce undisturbed. Whether the evolutionary benefit would be sufficient to maintain the more useful (to humans) abilities engineered into the yeast remains to be seen, but, as the yeast do with ethanol, there is a precedent for this type of process to be a mechanism by which the yeast maintain an apparently wasteful process as a means of outcompeting potential rival organisms.

I'm astounded. They're wasting good sugarcane, while Americans are reduced to drinking beverages sweetened with corn syrup! The power of the corn lobby has got to be defeated!

As far as powering cars is concerned, methyl alcohol can be made easily from things like leaves and sawdust, which don't compete with valuable food. That needs a replacement of the engine, though, not just minor adjustment, unlike ethanol. So they should ban new production of gasoline-fuelled cars, with methanol-fuelled cars being the closest thing left.

I'm astounded. They're wasting good sugarcane, while Americans are reduced to drinking beverages sweetened with corn syrup! The power of the corn lobby has got to be defeated!

As far as powering cars is concerned, methyl alcohol can be made easily from things like leaves and sawdust, which don't compete with valuable food. That needs a replacement of the engine, though, not just minor adjustment, unlike ethanol. So they should ban new production of gasoline-fuelled cars, with methanol-fuelled cars being the closest thing left.

Brazil shows that ethanol can be a viable fuel. We should be spending our genetic engineering knowhow on teaching yeast how to eat raw cellulose and sh*t ethanol instead of trying to get them to poop out a drop-in gasoline replacement. These yeastie beasties described in the article likely subsist on a diet of lab-grade sugar.